Rong Xu

Qinyong Wang, Zhenxiang Gao, Rong Xu

The biomedical field relies heavily on concept linking in various areas such as literature mining, graph alignment, information retrieval, question-answering, data, and knowledge integration. Although large language models (LLMs) have made significant strides in many natural language processing tasks, their effectiveness in biomedical concept mapping is yet to be fully explored. This research investigates a method that exploits the in-context learning (ICL) capabilities of large models for biomedical concept linking. The proposed approach adopts a two-stage retrieve-and-rank framework. Initially, biomedical concepts are embedded using language models, and then embedding similarity is utilized to retrieve the top candidates. These candidates' contextual information is subsequently incorporated into the prompt and processed by a large language model to re-rank the concepts. This approach achieved an accuracy of 90.% in BC5CDR disease entity normalization and 94.7% in chemical entity normalization, exhibiting a competitive performance relative to supervised learning methods. Further, it showed a significant improvement, with an over 20-point absolute increase in F1 score on an oncology matching dataset. Extensive qualitative assessments were conducted, and the benefits and potential shortcomings of using large language models within the biomedical domain were discussed. were discussed.

Qinyong Wang, Zhenxiang Gao, Rong Xu

Graph embedding methods such as Graph Neural Networks (GNNs) and Graph Transformers have contributed to the development of graph reasoning algorithms for various tasks on knowledge graphs. However, the lack of interpretability and explainability of graph embedding methods has limited their applicability in scenarios requiring explicit reasoning. In this paper, we introduce the Graph Agent (GA), an intelligent agent methodology of leveraging large language models (LLMs), inductive-deductive reasoning modules, and long-term memory for knowledge graph reasoning tasks. GA integrates aspects of symbolic reasoning and existing graph embedding methods to provide an innovative approach for complex graph reasoning tasks. By converting graph structures into textual data, GA enables LLMs to process, reason, and provide predictions alongside human-interpretable explanations. The effectiveness of the GA was evaluated on node classification and link prediction tasks. Results showed that GA reached state-of-the-art performance, demonstrating accuracy of 90.65%, 95.48%, and 89.32% on Cora, PubMed, and PrimeKG datasets, respectively. Compared to existing GNN and transformer models, GA offered advantages of explicit reasoning ability, free-of-training, easy adaption to various graph reasoning tasks

Jingqing Wang, Jiaxing Shang, Rong Xu et al.

Fake news detection has been a long-standing research focus in social networks. Recent studies suggest that incorporating sentiment information from both news content and user comments can enhance detection performance. However, existing approaches typically treat sentiment features as auxiliary signals, overlooking role differentiation, that is, the same sentiment polarity may originate from users with distinct roles, thereby limiting their ability to capture nuanced patterns for effective detection. To address this issue, we propose SARC, a Sentiment-Augmented Role Clustering framework which utilizes sentiment-enhanced deep clustering to identify user roles for improved fake news detection. The framework first generates user features through joint comment text representation (with BiGRU and Attention mechanism) and sentiment encoding. It then constructs a differentiable deep clustering module to automatically categorize user roles. Finally, unlike existing approaches which take fake news label as the unique supervision signal, we propose a joint optimization objective integrating role clustering and fake news detection to further improve the model performance. Experimental results on two benchmark datasets, RumourEval-19 and Weibo-comp, demonstrate that SARC achieves superior performance across all metrics compared to baseline models. The code is available at: https://github.com/jxshang/SARC.

Kyle Cox, Jiawei Xu, Yikun Han et al.

An interesting behavior in large language models (LLMs) is prompt sensitivity. When provided with different but semantically equivalent versions of the same prompt, models may produce very different distributions of answers. This suggests that the uncertainty reflected in a model's output distribution for one prompt may not reflect the model's uncertainty about the meaning of the prompt. We model prompt sensitivity as a type of generalization error, and show that sampling across the semantic ``concept space'' with paraphrasing perturbations improves uncertainty calibration without compromising accuracy. Additionally, we introduce a new metric for uncertainty decomposition in black-box LLMs that improves upon entropy-based decomposition by modeling semantic continuities in natural language generation. We show that this decomposition metric can be used to quantify how much LLM uncertainty is attributed to prompt sensitivity. Our work introduces a new way to improve uncertainty calibration in prompt-sensitive language models, and provides evidence that some LLMs fail to exhibit consistent general reasoning about the meanings of their inputs.

Yuchen Wang, Zhengyu Fang, Wei Du et al.

The opioid epidemic, referring to the growing hospitalizations and deaths because of overdose of opioid usage and addiction, has become a severe health problem in the United States. Many strategies have been developed by the federal and local governments and health communities to combat this crisis. Among them, improving our understanding of the epidemic through better health surveillance is one of the top priorities. In addition to direct testing, machine learning approaches may also allow us to detect opioid users by analyzing data from social media because many opioid users may choose not to do the tests but may share their experiences on social media anonymously. In this paper, we take advantage of recent advances in machine learning, collect and analyze user posts from a popular social network Reddit with the goal to identify opioid users. Posts from more than 1,000 users who have posted on three sub-reddits over a period of one month have been collected. In addition to the ones that contain keywords such as opioid, opiate, or heroin, we have also collected posts that contain slang words of opioid such as black or chocolate. We apply an attention-based bidirectional long short memory model to identify opioid users. Experimental results show that the approaches significantly outperform competitive algorithms in terms of F1-score. Furthermore, the model allows us to extract most informative words, such as opiate, opioid, and black, from posts via the attention layer, which provides more insights on how the machine learning algorithm works in distinguishing drug users from non-drug users.

Donghuo Zeng, Jianming Wu, Gen Hattori et al.

Learning common subspace is prevalent way in cross-modal retrieval to solve the problem of data from different modalities having inconsistent distributions and representations that cannot be directly compared. Previous cross-modal retrieval methods focus on projecting the cross-modal data into a common space by learning the correlation between them to bridge the modality gap. However, the rich semantic information in the video and the heterogeneous nature of audio-visual data leads to more serious heterogeneous gaps intuitively, which may lead to the loss of key semantic content of video with single clue by the previous methods when eliminating the modality gap, while the semantics of the categories may undermine the properties of the original features. In this work, we aim to learn effective audio-visual representations to support audio-visual cross-modal retrieval (AVCMR). We propose a novel model that maps audio-visual modalities into two distinct shared latent subspaces: explicit and implicit shared spaces. In particular, the explicit shared space is used to optimize pairwise correlations, where learned representations across modalities capture the commonalities of audio-visual pairs and reduce the modality gap. The implicit shared space is used to preserve the distinctive features between modalities by maintaining the discrimination of audio/video patterns from different semantic categories. Finally, the fusion of the features learned from the two latent subspaces is used for the similarity computation of the AVCMR task. The comprehensive experimental results on two audio-visual datasets demonstrate that our proposed model for using two different latent subspaces for audio-visual cross-modal learning is effective and significantly outperforms the state-of-the-art cross-modal models that learn features from a single subspace.

Colin L. Cooke, Fanjie Kong, Amey Chaware et al.

This paper introduces a new method of data-driven microscope design for virtual fluorescence microscopy. Our results show that by including a model of illumination within the first layers of a deep convolutional neural network, it is possible to learn task-specific LED patterns that substantially improve the ability to infer fluorescence image information from unstained transmission microscopy images. We validated our method on two different experimental setups, with different magnifications and different sample types, to show a consistent improvement in performance as compared to conventional illumination methods. Additionally, to understand the importance of learned illumination on inference task, we varied the dynamic range of the fluorescent image targets (from one to seven bits), and showed that the margin of improvement for learned patterns increased with the information content of the target. This work demonstrates the power of programmable optical elements at enabling better machine learning algorithm performance and at providing physical insight into next generation of machine-controlled imaging systems.

Zheng Ge, Zequn Jie, Xin Huang et al.

Detecting human bodies in highly crowded scenes is a challenging problem. Two main reasons result in such a problem: 1). weak visual cues of heavily occluded instances can hardly provide sufficient information for accurate detection; 2). heavily occluded instances are easier to be suppressed by Non-Maximum-Suppression (NMS). To address these two issues, we introduce a variant of two-stage detectors called PS-RCNN. PS-RCNN first detects slightly/none occluded objects by an R-CNN module (referred as P-RCNN), and then suppress the detected instances by human-shaped masks so that the features of heavily occluded instances can stand out. After that, PS-RCNN utilizes another R-CNN module specialized in heavily occluded human detection (referred as S-RCNN) to detect the rest missed objects by P-RCNN. Final results are the ensemble of the outputs from these two R-CNNs. Moreover, we introduce a High Resolution RoI Align (HRRA) module to retain as much of fine-grained features of visible parts of the heavily occluded humans as possible. Our PS-RCNN significantly improves recall and AP by 4.49% and 2.92% respectively on CrowdHuman, compared to the baseline. Similar improvements on Widerperson are also achieved by the PS-RCNN.